[Biopython-dev] SwissProt parser

Jeffrey Chang jchang at SMI.Stanford.EDU
Sat Nov 11 16:04:36 EST 2000

Heh.  It looks like ExPASy snuck in a new tag for us.  Thanks for the
update and patch!  It's now checked in.


On Sat, 11 Nov 2000, Brad Chapman wrote:

> Hello all;
>       I was writing docs for SwissProt, and noticed the parser
> breaking with some of the sequences I was playing around with. I don't 
> normally use SwissProt, so I have no idea if these entries are
> representative of the format or anything, but the following entries
> gave me problems: '023729', '023730', '023731' (some nice Chalcone
> synthases). 
> The problem was that there is a reference to the NCBI taxonomy id in
> the entries that the parser wasn't looking for. It occurs right after
> the organism info and looks like:
> OX   NCBI_TaxID=41205;
> Anyways, I modified the parser so that it would accept this, and added 
> the possible information to the sequence class. It seems to work okay
> with the entries I mentioned, and still passes the regression
> tests. The patch for this is attached.
> Please let me know if there are any problems with the patch or
> anything. Thanks!
> Brad

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